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Attempt to set 'rownames' on an object with no dimensions

Hello everyone! My name is Kseniia and I am new here!

I did encounter some problems while analyzing american gut data. Here is the code for it:

library(devtools)
devtools::install_github("zdk123/SpiecEasi")   
library(SpiecEasi) 
SpiecEasi.matrix <- spiec.easi(amgut1.filt,  
                           method = 'glasso',  
                           lambda.min.ratio = 1e-2,  
                           nlambda = 20,    
                           icov.select.params=list(rep.num=50))

The next line suppose to add OTU names to rows and columns

rownames(SpiecEasi.matrix$refit) <- colnames(amgut1.filt)

Then this error appeared: Error in rownames<-(*tmp*, value = c("OTU_1", "OTU_2", "OTU_3", "OTU_4", : attempt to set 'rownames' on an object with no dimensions

I understood that it appears because $refit is a list. But I don't know how to fix it. If anyone had the same error, I would greatly appreciate your help with its solution.

Thanks in advance! Kseniia

r microbiome spieceasi
• 8,311 views • link
updated by GenoMax GenoMax • written by ks.sholohova • ks.sholohova

hello everyone, I got the same error for a function immuCellAI_new;

result <- ImmuCellAI_new(countData = expr_data_log22, data_type = "rnaseq", group_tag = 1, response_tag = 0, customer = 0)
Error in `rownames<-`(`*tmp*`, value = colnames(countData)) : 
  attempt to set 'rownames' on an object with no dimensions,  CountDATA is a matrix with genes expression, the colnames express the sample and the rownames are the gene

, how to fix that, when I run this commande, I got value; dn NULL (empty, nd )L, value chr[1:1082] et x NULL (empty)

• 0 views • link
updated by GenoMax GenoMax • written by elbakri.fatimazahrae • elbakri.fatimazahrae

1 answer

Try this:

rownames(SpiecEasi.matrix$refit$stars) <- colnames(amgut1.filt)
• 0 views • link
written by andres.firrincieli andres.firrincieli

Thank you very much, Andres! Now everything perfectly works.

I just want to make sure please that I understand the concept, if you don't mind. So, SpiecEasi.matrix$refit is a list. That's why I got this error. Then by using SpiecEasi.matrix$refit$stars I refer to numeric object that is dimensional already and, hence, it works.

Have a nice day!

• 0 views • link
written by ks.sholohova • ks.sholohova

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